BoutrosRNAi2002: RNAi data on Drosophila innate immune response

In nem: (Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

Description

Data from a study on innate immune response in Drosophila (Boutros et al, 2002). Selectively removing signaling components by RNAi blocked induction of all, or only parts, of the transcriptional response to LPS. The nested structure of perturbation effects allows to reconstruct a branching in the Imd pathway.

Usage

data(BoutrosRNAi2002)

Format

BoutrosRNAiExpression: data matrix: 14010 x 16\ BoutrosRNAiDiscrete: binary matrix: 68 x 16\ BoutrosRNAiDens: data matrix: 68 x 4\ BoutrosRNAiLods: data matrix: 68 x 4\ BoutrosRNAiLogFC: data matrix: 68 x 4

Details

The dataset consists of 16 Affymetrix-microarrays: 4 replicates of control experiments without LPS and without RNAi (negative controls), 4 replicates of expression profiling after stimulation with LPS but without RNAi (positive controls), and 2 replicates each of expression profiling after applying LPS and silencing one of the four candidate genes tak, key, rel, and mkk4/hep.

BoutrosRNAiExpression: For preprocessing we performed normalization on probe level using a variance stabilizing transformation (Huber et al, 2002), and probe set summarization using a median polish fit of an additive model (Irizarry et al, 2003).

BoutrosRNAiDiscrete: contains only the 68 genes more than two-fold up-regulated between negative and positive controls. The continuous expression values are discretized to 1 (effect: closer to negative controls) and 0 (no effect: closer to positive controls).

BoutrosRNAiDens: log p-value density matrix for the 68 genes with more than two-fold up-regulated between negative and positive controls.

BoutrosRNAiLods: B-value matrix for the 68 genes with more than two-fold up-regulated between negative and positive controls.

BoutrosRNAiLogFC: matrix with log fold changes

References

Boutros M, Agaisse H, Perrimon N, Sequential activation of signaling pathways during innate immune responses in Drosophila. Developmental Cell. 3(5):711-722, 2002

See Also

nem.discretize

Examples

    data("BoutrosRNAi2002")
    dim(BoutrosRNAiExpression)
    dim(BoutrosRNAiDiscrete)      

nem documentation built on Oct. 31, 2019, 2:12 a.m.